Excitation energy transfer: Study with non-Markovian dynamics

In this paper, we investigate the non-Markovian dynamics of a model to mimic the excitation energy transfer (EET) between chromophores in photosynthesis systems. The numerical path integral method is used. This method includes the non-Markovian effects of the environmental affects and it does not need the perturbation approximation in solving the dynamics of systems of interest. It implies that the coherence helps the EET between chromophores through lasting the transfer time rather than enhances the transfer rate of the EET. In particular, the non-Markovian environment greatly increase the efficiency of the EET in the photosynthesis systems.Comment: 5 pages, 5 figure

Molecular Mechanics Simulations and Improved Tight-binding Hamiltonians for Artificial Light Harvesting Systems: Predicting Geometric Distributions, Disorder, and Spectroscopy of Chromophores in a Protein Environment

We present molecular mechanics {and spectroscopic} calculations on prototype artificial light harvesting systems consisting of chromophores attached to a tobacco mosaic virus (TMV) protein scaffold. These systems have been synthesized and characterized spectroscopically, but information about the microscopic configurations and geometry of these TMV-templated chromophore assemblies is largely unknown. We use a Monte Carlo conformational search algorithm to determine the preferred positions and orientations of two chromophores, Coumarin 343 together with its linker, and Oregon Green 488, when these are attached at two different sites (104 and 123) on the TMV protein. The resulting geometric information shows that the extent of disorder and aggregation properties, and therefore the optical properties of the TMV-templated chromophore assembly, are highly dependent on the choice of chromophores and protein site to which they are bound. We used the results of the conformational search as geometric parameters together with an improved tight-binding Hamiltonian to simulate the linear absorption spectra and compare with experimental spectral measurements. The ideal dipole approximation to the Hamiltonian is not valid since the distance between chromophores can be very small. We found that using the geometries from the conformational search is necessary to reproduce the features of the experimental spectral peaks

Short to long-range charge-transfer excitations in the zincbacteriochlorin-bacteriochlorin complex: a Bethe-Salpeter study

We study using the Bethe-Salpeter formalism the excitation energies of the zincbacteriochlorinbacteriochlorin dyad, a paradigmatic photosynthetic complex. In great contrast with standard timedependent density functional theory calculations with (semi)local kernels, charge transfer excitations are correctly located above the intramolecular Q-bands transitions found to be in excellent agreement with experiment. Further, the asymptotic Coulomb behavior towards the true quasiparticle gap for charge transfer excitations at long distance is correctly reproduced, showing that the present scheme allows to study with the same accuracy intramolecular and charge transfer excitations at various spatial range and screening environment without any adjustable parameter.Comment: 5 pages, 2 figures, 1 tabl

Structural information on the light-harvesting complex II of green plants that can be depichered from polarized absorption characteristics.

The atomic model of light-harvesting complex II of green plants (LHCII) reveals a densely packed arrangement of 12 chlorophylls and two carotenoids. At the current resolution of 3.4 Angstrom chlorophylls can only be modeled as ''naked'' tetrapyrrole rings. Consequently, definitive assignments of the identities of the chlorophylls (chlorophyll a or chlorophyll b) and the directions of the transition dipole moments are obstructed. These uncertainties lead to a large number of possible configurations, and a detailed understanding of the structure-function relationship is obscured. It is demonstrated that a large reduction in the number of possible configurations and a considerable amount of additional structural information can be obtained by deciphering global features of the polarized absorption spectra within the context of exciton calculations. It is shown that only a limited number of configurations are able to explain the global features of the linear and circular dichroism spectra of LHCII. Assuming that the preliminary assignment of the identities of the 12 chlorophylls by Kuhlbrandt and co-workers is correct, it is possible to deduce the most likely orientations for most of the chlorophylls. The information presented in this study on the most likely orientations will be important for a detailed understanding of the relation between the structure and spectroscopy

Spectral broadening of interacting pigments: Polarized absorption by photosynthetic proteins.

Excitonic interaction between pigment molecules is largely responsible for the static and dynamic spectroscopic properties of photosynthetic pigment-proteins. This paper provides a new description of its effect on polarized absorption spectroscopy, in particular on circular dichroism (CD). We investigate excitonic spectra of finite width and use "spectral moments" to compare 1) inhomogeneously broadened excitonic spectra, 2) spectra that are (homogeneously broadened by vibrations or electron-phonon interaction, and 3) spectra that are simulated by applying convolution after the interaction has been evaluated. Two cases are distinguished. If the excitonic splitting is smaller than the width of the interacting absorption bands, the broadening of the excitonic spectrum can be approximated by a convolution approach, although a correction is necessary for CD spectra. If the excitonic splitting exceeds the bandwidth, the well-known exchange narrowing occurs. We demonstrate that this is accompanied by redistribution of dipole strength and spectral shifts. The magnitude of a CD spectrum is conveniently expressed by its first spectral moment. As will be shown, this is independent of spectral broadening as well as dispersive shifts induced by pigment-protein interactions. Consequently, it provides a simple tool to relate the experimental CD spectrum of a pigment complex to the excitonic interactions from which it originates. To illustrate the potential of the presented framework, the spectroscopy of the LH2 pigment-protein complex from purple bacteria is analyzed and compared for dimer-like and ring-like structures. Furthermore, it is demonstrated that the variability of the CD of chlorosomes from green bacteria can be explained by small changes in the structure of their cylindrical bacteriochlorophyll c subunits

Yang-Yang thermodynamics on an atom chip

We investigate the behavior of a weakly interacting nearly one-dimensional (1D) trapped Bose gas at finite temperature. We perform in situ measurements of spatial density profiles and show that they are very well described by a model based on exact solutions obtained using the Yang-Yang thermodynamic formalism, in a regime where other, approximate theoretical approaches fail. We use Bose-gas focusing [Shvarchuck etal., Phys. Rev. Lett. 89, 270404 (2002)] to probe the axial momentum distribution of the gas, and find good agreement with the in situ results.Comment: extended introduction and conclusions, and minor changes throughout; accepted for publication in Phys. Rev. Let

Cold trapped atoms detected with evanescent waves

We demonstrate the in situ detection of cold 87 Rb atoms near a dielectric surface using the absorption of a weak, resonant evanescent wave. We have used this technique in time of flight experiments determining the density of atoms falling on the surface. A quantitative understanding of the measured curve was obtained using a detailed calculation of the evanescent intensity distribution. We have also used it to detect atoms trapped near the surface in a standing-wave optical dipole potential. This trap was loaded by inelastic bouncing on a strong, repulsive evanescent potential. We estimate that we trap 1.5 x 10 4 atoms at a density 100 times higher than the falling atoms.Comment: 5 pages, 3 figure

Probing quantum-mechanical level repulsion in disordered systems by means of time-resolved selectively-excited resonance fluorescence

We argue that the time-resolved spectrum of selectively-excited resonance fluorescence at low temperature provides a tool for probing the quantum-mechanical level repulsion in the Lifshits tail of the electronic density of states in a wide variety of disordered materials. The technique, based on detecting the fast growth of a fluorescence peak that is red-shifted relative to the excitation frequency, is demonstrated explicitly by simulations on linear Frenkel exciton chains.Comment: 4 pages, 4 figures, to appear in Phys. Rev. Let

Light-harvesting in bacteria exploits a critical interplay between transport and trapping dynamics

Light-harvesting bacteria Rhodospirillum Photometricum were recently found to adopt strikingly different architectures depending on illumination conditions. We present analytic and numerical calculations which explain this observation by quantifying a dynamical interplay between excitation transfer kinetics and reaction center cycling. High light-intensity membranes (HLIM) exploit dissipation as a photo-protective mechanism, thereby safeguarding a steady supply of chemical energy, while low light-intensity membranes (LLIM) efficiently process unused illumination intensity by channelling it to open reaction centers. More generally, our analysis elucidates and quantifies the trade-offs in natural network design for solar energy conversion.Comment: 4 pages and 4 figures. Accepted for publication in Physical Review Letters

Box traps on an atom chip for one-dimensional quantum gases

We present the implementation of tailored trapping potentials for ultracold gases on an atom chip. We realize highly elongated traps with box-like confinement along the long, axial direction combined with conventional harmonic confinement along the two radial directions. The design, fabrication and characterization of the atom chip and the box traps is described. We load ultracold ($\lesssim1 \mu$K) clouds of $^{87}$Rb in a box trap, and demonstrate Bose-gas focusing as a means to characterize these atomic clouds in arbitrarily shaped potentials. Our results show that box-like axial potentials on atom chips are very promising for studies of one-dimensional quantum gases.Comment: 9 pages 4 figure